Starting phenix.real_space_refine on Mon Feb 19 18:17:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xm4_22255/02_2024/6xm4_22255.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.963 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 110 5.16 5 C 16158 2.51 5 N 4143 2.21 5 O 4987 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 200": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 281": "OE1" <-> "OE2" Residue "A ARG 319": "NH1" <-> "NH2" Residue "A GLU 324": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A GLU 340": "OE1" <-> "OE2" Residue "A ASP 364": "OD1" <-> "OD2" Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 405": "OD1" <-> "OD2" Residue "A PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 457": "NH1" <-> "NH2" Residue "A GLU 484": "OE1" <-> "OE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 541": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 565": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 568": "OD1" <-> "OD2" Residue "A ASP 574": "OD1" <-> "OD2" Residue "A ASP 578": "OD1" <-> "OD2" Residue "A ASP 614": "OD1" <-> "OD2" Residue "A GLU 619": "OE1" <-> "OE2" Residue "A ASP 627": "OD1" <-> "OD2" Residue "A ARG 634": "NH1" <-> "NH2" Residue "A GLU 748": "OE1" <-> "OE2" Residue "A PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1107": "NH1" <-> "NH2" Residue "A GLU 1111": "OE1" <-> "OE2" Residue "A ASP 1118": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 40": "OD1" <-> "OD2" Residue "B PHE 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 96": "OE1" <-> "OE2" Residue "B PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 273": "NH1" <-> "NH2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B ASP 364": "OD1" <-> "OD2" Residue "B TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 423": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 516": "OE1" <-> "OE2" Residue "B PHE 559": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 571": "OD1" <-> "OD2" Residue "B TYR 612": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 627": "OD1" <-> "OD2" Residue "B ARG 634": "NH1" <-> "NH2" Residue "B ASP 663": "OD1" <-> "OD2" Residue "B TYR 695": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 847": "NH1" <-> "NH2" Residue "B GLU 868": "OE1" <-> "OE2" Residue "B PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 1107": "NH1" <-> "NH2" Residue "B GLU 1111": "OE1" <-> "OE2" Residue "B PHE 1121": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 1139": "OD1" <-> "OD2" Residue "C ASP 111": "OD1" <-> "OD2" Residue "C PHE 133": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 220": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 273": "NH1" <-> "NH2" Residue "C ASP 290": "OD1" <-> "OD2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 403": "NH1" <-> "NH2" Residue "C ASP 442": "OD1" <-> "OD2" Residue "C ARG 457": "NH1" <-> "NH2" Residue "C ASP 467": "OD1" <-> "OD2" Residue "C PHE 490": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 619": "OE1" <-> "OE2" Residue "C ARG 634": "NH1" <-> "NH2" Residue "C GLU 654": "OE1" <-> "OE2" Residue "C TYR 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 661": "OE1" <-> "OE2" Residue "C PHE 718": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 839": "OD1" <-> "OD2" Residue "C ASP 950": "OD1" <-> "OD2" Residue "C ASP 979": "OD1" <-> "OD2" Residue "C ASP 985": "OD1" <-> "OD2" Residue "C GLU 1017": "OE1" <-> "OE2" Residue "C PHE 1075": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 1089": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 1111": "OE1" <-> "OE2" Residue "C ASP 1118": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 25398 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 8103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1037, 8103 Classifications: {'peptide': 1037} Link IDs: {'PTRANS': 51, 'TRANS': 985} Chain breaks: 7 Chain: "B" Number of atoms: 8259 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 Conformer: "B" Number of residues, atoms: 1058, 8253 Classifications: {'peptide': 1058} Link IDs: {'PTRANS': 52, 'TRANS': 1005} Chain breaks: 5 bond proxies already assigned to first conformer: 8435 Chain: "C" Number of atoms: 8182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1048, 8182 Classifications: {'peptide': 1048} Link IDs: {'PTRANS': 52, 'TRANS': 995} Chain breaks: 7 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "O" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "P" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "Q" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "S" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "T" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "U" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 154 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 154 Unusual residues: {'NAG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 11 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 11 Chain: "B" Number of atoms: 112 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 112 Unusual residues: {'NAG': 8} Classifications: {'undetermined': 8} Link IDs: {None: 7} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 24 Unresolved non-hydrogen chiralities: 8 Chain: "C" Number of atoms: 84 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 84 Unusual residues: {'NAG': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 18 Unresolved non-hydrogen chiralities: 6 Time building chain proxies: 15.99, per 1000 atoms: 0.63 Number of scatterers: 25398 At special positions: 0 Unit cell: (138.55, 138.55, 198.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 110 16.00 O 4987 8.00 N 4143 7.00 C 16158 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=40, symmetry=0 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.05 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.02 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.04 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.04 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 760 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.02 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.05 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 760 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.05 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.01 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.06 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.03 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 738 " - pdb=" SG CYS C 760 " distance=2.04 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.02 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 2 " " NAG P 1 " - " NAG P 2 " " NAG Q 1 " - " NAG Q 2 " " NAG R 1 " - " NAG R 2 " " NAG S 1 " - " NAG S 2 " " NAG T 1 " - " NAG T 2 " " NAG U 1 " - " NAG U 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 603 " " NAG A1307 " - " ASN A 616 " " NAG A1308 " - " ASN A 657 " " NAG A1309 " - " ASN A 709 " " NAG A1310 " - " ASN A1074 " " NAG A1311 " - " ASN A 165 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 282 " " NAG B1303 " - " ASN B 343 " " NAG B1304 " - " ASN B 603 " " NAG B1305 " - " ASN B 616 " " NAG B1306 " - " ASN B 657 " " NAG B1307 " - " ASN B 709 " " NAG B1308 " - " ASN B 165 " " NAG C1301 " - " ASN C 61 " " NAG C1302 " - " ASN C 282 " " NAG C1303 " - " ASN C 331 " " NAG C1304 " - " ASN C 616 " " NAG C1305 " - " ASN C 657 " " NAG C1306 " - " ASN C 709 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A1098 " " NAG H 1 " - " ASN A1134 " " NAG I 1 " - " ASN B 234 " " NAG J 1 " - " ASN B 331 " " NAG K 1 " - " ASN B 717 " " NAG L 1 " - " ASN B 801 " " NAG M 1 " - " ASN B1074 " " NAG N 1 " - " ASN B1098 " " NAG O 1 " - " ASN B1134 " " NAG P 1 " - " ASN C 343 " " NAG Q 1 " - " ASN C 717 " " NAG R 1 " - " ASN C 801 " " NAG S 1 " - " ASN C1074 " " NAG T 1 " - " ASN C1098 " " NAG U 1 " - " ASN C1134 " Time building additional restraints: 9.11 Conformation dependent library (CDL) restraints added in 5.6 seconds 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5898 Finding SS restraints... Secondary structure from input PDB file: 60 helices and 47 sheets defined 22.7% alpha, 25.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.24 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.619A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.606A pdb=" N ASN A 370 " --> pdb=" O SER A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 619 through 624 Processing helix chain 'A' and resid 625 through 629 Processing helix chain 'A' and resid 633 through 637 Processing helix chain 'A' and resid 737 through 743 Processing helix chain 'A' and resid 749 through 754 removed outlier: 3.539A pdb=" N LEU A 754 " --> pdb=" O SER A 750 " (cutoff:3.500A) Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 758 through 783 removed outlier: 3.778A pdb=" N GLN A 762 " --> pdb=" O SER A 758 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N LEU A 763 " --> pdb=" O PHE A 759 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ASN A 764 " --> pdb=" O CYS A 760 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU A 767 " --> pdb=" O LEU A 763 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 778 " --> pdb=" O GLN A 774 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N VAL A 781 " --> pdb=" O ASN A 777 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 826 removed outlier: 3.778A pdb=" N ASN A 824 " --> pdb=" O ASP A 820 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N LYS A 825 " --> pdb=" O LEU A 821 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N VAL A 826 " --> pdb=" O LEU A 822 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 855 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 897 through 908 removed outlier: 3.544A pdb=" N TYR A 904 " --> pdb=" O MET A 900 " (cutoff:3.500A) Processing helix chain 'A' and resid 913 through 918 removed outlier: 3.647A pdb=" N TYR A 917 " --> pdb=" O GLN A 913 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 939 removed outlier: 3.619A pdb=" N GLN A 935 " --> pdb=" O ILE A 931 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ASP A 936 " --> pdb=" O GLY A 932 " (cutoff:3.500A) Processing helix chain 'A' and resid 945 through 965 removed outlier: 4.022A pdb=" N VAL A 951 " --> pdb=" O LYS A 947 " (cutoff:3.500A) removed outlier: 3.851A pdb=" N VAL A 952 " --> pdb=" O LEU A 948 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 981 removed outlier: 3.571A pdb=" N ILE A 980 " --> pdb=" O VAL A 976 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU A 981 " --> pdb=" O LEU A 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 976 through 981' Processing helix chain 'A' and resid 985 through 1033 removed outlier: 3.734A pdb=" N GLU A 990 " --> pdb=" O PRO A 986 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N VAL A 991 " --> pdb=" O PRO A 987 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ARG A 995 " --> pdb=" O VAL A 991 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLU A1017 " --> pdb=" O ILE A1013 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU A1024 " --> pdb=" O ALA A1020 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL A1033 " --> pdb=" O MET A1029 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 303 removed outlier: 3.599A pdb=" N GLU B 298 " --> pdb=" O ASP B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 370 Processing helix chain 'B' and resid 416 through 422 removed outlier: 3.608A pdb=" N TYR B 421 " --> pdb=" O LYS B 417 " (cutoff:3.500A) Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.739A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 619 through 624 Processing helix chain 'B' and resid 625 through 629 removed outlier: 3.529A pdb=" N LEU B 629 " --> pdb=" O ALA B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 633 through 637 removed outlier: 3.571A pdb=" N SER B 637 " --> pdb=" O ARG B 634 " (cutoff:3.500A) Processing helix chain 'B' and resid 737 through 744 removed outlier: 3.519A pdb=" N GLY B 744 " --> pdb=" O MET B 740 " (cutoff:3.500A) Processing helix chain 'B' and resid 749 through 754 removed outlier: 3.507A pdb=" N LEU B 754 " --> pdb=" O SER B 750 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 783 removed outlier: 3.800A pdb=" N GLN B 762 " --> pdb=" O SER B 758 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ALA B 766 " --> pdb=" O GLN B 762 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N THR B 778 " --> pdb=" O GLN B 774 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL B 781 " --> pdb=" O ASN B 777 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 823 Processing helix chain 'B' and resid 831 through 839 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 897 through 908 Processing helix chain 'B' and resid 913 through 919 removed outlier: 3.653A pdb=" N TYR B 917 " --> pdb=" O GLN B 913 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 939 Processing helix chain 'B' and resid 945 through 965 removed outlier: 4.111A pdb=" N VAL B 951 " --> pdb=" O LYS B 947 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL B 952 " --> pdb=" O LEU B 948 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 962 " --> pdb=" O ALA B 958 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 981 removed outlier: 3.664A pdb=" N ILE B 980 " --> pdb=" O VAL B 976 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LEU B 981 " --> pdb=" O LEU B 977 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 976 through 981' Processing helix chain 'B' and resid 985 through 1032 removed outlier: 4.648A pdb=" N VAL B 991 " --> pdb=" O PRO B 987 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 995 " --> pdb=" O VAL B 991 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLU B1017 " --> pdb=" O ILE B1013 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 303 Processing helix chain 'C' and resid 338 through 343 Processing helix chain 'C' and resid 383 through 390 removed outlier: 3.608A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 619 through 624 removed outlier: 3.508A pdb=" N ALA C 623 " --> pdb=" O GLU C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 634 through 638 removed outlier: 3.889A pdb=" N SER C 637 " --> pdb=" O ARG C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 737 through 743 Processing helix chain 'C' and resid 746 through 751 removed outlier: 3.702A pdb=" N ASN C 751 " --> pdb=" O THR C 747 " (cutoff:3.500A) Processing helix chain 'C' and resid 752 through 757 removed outlier: 3.569A pdb=" N GLN C 755 " --> pdb=" O LEU C 752 " (cutoff:3.500A) Processing helix chain 'C' and resid 758 through 783 removed outlier: 3.823A pdb=" N GLN C 762 " --> pdb=" O SER C 758 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR C 778 " --> pdb=" O GLN C 774 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL C 781 " --> pdb=" O ASN C 777 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 823 Processing helix chain 'C' and resid 835 through 840 removed outlier: 4.024A pdb=" N ASP C 839 " --> pdb=" O GLN C 836 " (cutoff:3.500A) Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 897 through 908 removed outlier: 3.569A pdb=" N TYR C 904 " --> pdb=" O MET C 900 " (cutoff:3.500A) Processing helix chain 'C' and resid 913 through 919 Processing helix chain 'C' and resid 919 through 940 removed outlier: 3.514A pdb=" N ASP C 936 " --> pdb=" O GLY C 932 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N SER C 939 " --> pdb=" O GLN C 935 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N SER C 940 " --> pdb=" O ASP C 936 " (cutoff:3.500A) Processing helix chain 'C' and resid 945 through 965 removed outlier: 4.057A pdb=" N VAL C 951 " --> pdb=" O LYS C 947 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 952 " --> pdb=" O LEU C 948 " (cutoff:3.500A) Processing helix chain 'C' and resid 976 through 980 removed outlier: 3.657A pdb=" N ILE C 980 " --> pdb=" O LEU C 977 " (cutoff:3.500A) Processing helix chain 'C' and resid 989 through 1033 removed outlier: 3.997A pdb=" N ILE C 993 " --> pdb=" O ALA C 989 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ARG C 995 " --> pdb=" O VAL C 991 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C1017 " --> pdb=" O ILE C1013 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER C1030 " --> pdb=" O ALA C1026 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 30 removed outlier: 3.516A pdb=" N VAL A 267 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N PHE A 201 " --> pdb=" O ASP A 228 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ASP A 228 " --> pdb=" O PHE A 201 " (cutoff:3.500A) removed outlier: 7.045A pdb=" N ILE A 203 " --> pdb=" O LEU A 226 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 7.621A pdb=" N THR A 274 " --> pdb=" O ASP A 290 " (cutoff:3.500A) removed outlier: 5.195A pdb=" N ASP A 290 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N LEU A 276 " --> pdb=" O ALA A 288 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA A 288 " --> pdb=" O LEU A 276 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N LYS A 278 " --> pdb=" O THR A 286 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.611A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 141 through 142 removed outlier: 6.014A pdb=" N LEU A 141 " --> pdb=" O LEU A 244 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.638A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 324 through 325 removed outlier: 7.303A pdb=" N GLU A 324 " --> pdb=" O ASN A 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.297A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.121A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB1, first strand: chain 'A' and resid 542 through 543 Processing sheet with id=AB2, first strand: chain 'A' and resid 551 through 554 removed outlier: 5.310A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA A 575 " --> pdb=" O GLY A 566 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.346A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.847A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 704 removed outlier: 6.643A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N LYS B 790 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASN A 703 " --> pdb=" O LYS B 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR A1067 " --> pdb=" O HIS A1048 " (cutoff:3.500A) removed outlier: 5.862A pdb=" N HIS A1048 " --> pdb=" O TYR A1067 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 711 through 728 removed outlier: 6.577A pdb=" N SER A 711 " --> pdb=" O THR A1076 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N THR A1076 " --> pdb=" O SER A 711 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ALA A 713 " --> pdb=" O ASN A1074 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N ASN A1074 " --> pdb=" O ALA A 713 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N GLU A1072 " --> pdb=" O PRO A 715 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.644A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 790 removed outlier: 6.043A pdb=" N ILE A 788 " --> pdb=" O ASN C 703 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'A' and resid 1120 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 29 through 31 removed outlier: 3.874A pdb=" N SER B 60 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N SER B 94 " --> pdb=" O ARG B 190 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N ARG B 190 " --> pdb=" O SER B 94 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLU B 96 " --> pdb=" O ASN B 188 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ASN B 188 " --> pdb=" O GLU B 96 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N ILE B 203 " --> pdb=" O LEU B 226 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 48 through 55 removed outlier: 3.517A pdb=" N ASP B 53 " --> pdb=" O ARG B 273 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N ASN B 280 " --> pdb=" O ILE B 285 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 285 " --> pdb=" O ASN B 280 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 84 through 85 removed outlier: 3.697A pdb=" N GLY B 103 " --> pdb=" O LEU B 241 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 311 through 318 removed outlier: 7.139A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN B 317 " --> pdb=" O GLY B 593 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N GLY B 593 " --> pdb=" O ASN B 317 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.622A pdb=" N ASN B 354 " --> pdb=" O SER B 399 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N SER B 399 " --> pdb=" O ASN B 354 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER B 514 " --> pdb=" O TYR B 396 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N VAL B 510 " --> pdb=" O PHE B 400 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AC7, first strand: chain 'B' and resid 538 through 543 removed outlier: 3.630A pdb=" N ILE B 587 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N GLY B 566 " --> pdb=" O ASP B 574 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N PHE B 565 " --> pdb=" O PHE C 43 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.315A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.859A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N SER B 691 " --> pdb=" O GLN B 675 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLN B 675 " --> pdb=" O SER B 691 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N SER B 673 " --> pdb=" O ILE B 693 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE B 670 " --> pdb=" O ILE B 666 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 701 through 704 removed outlier: 6.567A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N LYS C 790 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 7.365A pdb=" N ASN B 703 " --> pdb=" O LYS C 790 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR B1067 " --> pdb=" O HIS B1048 " (cutoff:3.500A) removed outlier: 5.808A pdb=" N HIS B1048 " --> pdb=" O TYR B1067 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 711 through 728 removed outlier: 6.676A pdb=" N SER B 711 " --> pdb=" O THR B1076 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N THR B1076 " --> pdb=" O SER B 711 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ALA B 713 " --> pdb=" O ASN B1074 " (cutoff:3.500A) removed outlier: 7.136A pdb=" N ASN B1074 " --> pdb=" O ALA B 713 " (cutoff:3.500A) removed outlier: 6.386A pdb=" N GLU B1072 " --> pdb=" O PRO B 715 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.529A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER B 735 " --> pdb=" O THR B 859 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 1120 through 1125 removed outlier: 4.583A pdb=" N ALA B1087 " --> pdb=" O SER B1123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 29 through 31 removed outlier: 3.755A pdb=" N THR C 29 " --> pdb=" O VAL C 62 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL C 62 " --> pdb=" O THR C 29 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER C 31 " --> pdb=" O SER C 60 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER C 60 " --> pdb=" O SER C 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'C' and resid 36 through 37 removed outlier: 7.228A pdb=" N VAL C 36 " --> pdb=" O LEU C 223 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N ILE C 203 " --> pdb=" O LEU C 226 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N ASP C 228 " --> pdb=" O PHE C 201 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N PHE C 201 " --> pdb=" O ASP C 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS C 206 " --> pdb=" O GLU C 191 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N TYR C 91 " --> pdb=" O GLY C 268 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 93 " --> pdb=" O TYR C 266 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 48 through 55 removed outlier: 7.590A pdb=" N THR C 274 " --> pdb=" O ASP C 290 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASP C 290 " --> pdb=" O THR C 274 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N LEU C 276 " --> pdb=" O ALA C 288 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ALA C 288 " --> pdb=" O LEU C 276 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N LYS C 278 " --> pdb=" O THR C 286 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 169 through 171 removed outlier: 3.553A pdb=" N LEU C 117 " --> pdb=" O PHE C 106 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ASN C 121 " --> pdb=" O ARG C 102 " (cutoff:3.500A) removed outlier: 7.191A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN C 239 " --> pdb=" O ILE C 105 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLY C 107 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ARG C 237 " --> pdb=" O GLY C 107 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 311 through 319 removed outlier: 7.055A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) removed outlier: 4.624A pdb=" N ASN C 317 " --> pdb=" O GLY C 593 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N GLY C 593 " --> pdb=" O ASN C 317 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N GLY C 594 " --> pdb=" O GLN C 613 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 324 through 325 removed outlier: 7.215A pdb=" N GLU C 324 " --> pdb=" O ASN C 540 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LYS C 378 " --> pdb=" O VAL C 433 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.597A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N ASN C 394 " --> pdb=" O GLU C 516 " (cutoff:3.500A) removed outlier: 5.047A pdb=" N GLU C 516 " --> pdb=" O ASN C 394 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 452 through 454 removed outlier: 3.857A pdb=" N TYR C 453 " --> pdb=" O GLN C 493 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLN C 493 " --> pdb=" O TYR C 453 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'C' and resid 473 through 474 removed outlier: 4.229A pdb=" N TYR C 473 " --> pdb=" O TYR C 489 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N TYR C 489 " --> pdb=" O TYR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE5 Processing sheet with id=AE6, first strand: chain 'C' and resid 551 through 554 removed outlier: 5.622A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N ALA C 575 " --> pdb=" O GLY C 566 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.778A pdb=" N SER C 691 " --> pdb=" O GLN C 675 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN C 675 " --> pdb=" O SER C 691 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ILE C 670 " --> pdb=" O ILE C 666 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLY C1059 " --> pdb=" O ALA C1056 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N TYR C1067 " --> pdb=" O HIS C1048 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N HIS C1048 " --> pdb=" O TYR C1067 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 711 through 728 removed outlier: 6.605A pdb=" N SER C 711 " --> pdb=" O THR C1076 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N THR C1076 " --> pdb=" O SER C 711 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N ALA C 713 " --> pdb=" O ASN C1074 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N ASN C1074 " --> pdb=" O ALA C 713 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N GLU C1072 " --> pdb=" O PRO C 715 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'C' and resid 734 through 736 removed outlier: 3.504A pdb=" N SER C 735 " --> pdb=" O THR C 859 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'C' and resid 1120 through 1125 removed outlier: 4.905A pdb=" N ALA C1087 " --> pdb=" O SER C1123 " (cutoff:3.500A) 849 hydrogen bonds defined for protein. 2339 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 11.94 Time building geometry restraints manager: 9.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.34: 7983 1.34 - 1.48: 7186 1.48 - 1.61: 10656 1.61 - 1.75: 1 1.75 - 1.89: 133 Bond restraints: 25959 Sorted by residual: bond pdb=" C GLN A1142 " pdb=" N PRO A1143 " ideal model delta sigma weight residual 1.334 1.402 -0.068 2.34e-02 1.83e+03 8.39e+00 bond pdb=" C1 NAG B1308 " pdb=" O5 NAG B1308 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.59e+00 bond pdb=" C1 NAG K 2 " pdb=" O5 NAG K 2 " ideal model delta sigma weight residual 1.406 1.461 -0.055 2.00e-02 2.50e+03 7.52e+00 bond pdb=" C1 NAG G 2 " pdb=" O5 NAG G 2 " ideal model delta sigma weight residual 1.406 1.460 -0.054 2.00e-02 2.50e+03 7.35e+00 bond pdb=" C VAL C 620 " pdb=" N PRO C 621 " ideal model delta sigma weight residual 1.337 1.371 -0.033 1.24e-02 6.50e+03 7.26e+00 ... (remaining 25954 not shown) Histogram of bond angle deviations from ideal: 94.23 - 102.30: 54 102.30 - 110.36: 6983 110.36 - 118.43: 13083 118.43 - 126.49: 14915 126.49 - 134.55: 305 Bond angle restraints: 35340 Sorted by residual: angle pdb=" C SER A 31 " pdb=" N PHE A 32 " pdb=" CA PHE A 32 " ideal model delta sigma weight residual 121.54 134.35 -12.81 1.91e+00 2.74e-01 4.49e+01 angle pdb=" N THR B 415 " pdb=" CA THR B 415 " pdb=" C THR B 415 " ideal model delta sigma weight residual 108.34 115.25 -6.91 1.31e+00 5.83e-01 2.78e+01 angle pdb=" N PRO A 986 " pdb=" CA PRO A 986 " pdb=" C PRO A 986 " ideal model delta sigma weight residual 110.70 116.82 -6.12 1.22e+00 6.72e-01 2.52e+01 angle pdb=" N CYS C 432 " pdb=" CA CYS C 432 " pdb=" C CYS C 432 " ideal model delta sigma weight residual 109.95 117.22 -7.27 1.59e+00 3.96e-01 2.09e+01 angle pdb=" C GLY B 842 " pdb=" N ASP B 843 " pdb=" CA ASP B 843 " ideal model delta sigma weight residual 121.54 130.27 -8.73 1.91e+00 2.74e-01 2.09e+01 ... (remaining 35335 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 14548 17.89 - 35.78: 1350 35.78 - 53.66: 265 53.66 - 71.55: 62 71.55 - 89.44: 28 Dihedral angle restraints: 16253 sinusoidal: 7092 harmonic: 9161 Sorted by residual: dihedral pdb=" CB CYS A 538 " pdb=" SG CYS A 538 " pdb=" SG CYS A 590 " pdb=" CB CYS A 590 " ideal model delta sinusoidal sigma weight residual 93.00 168.42 -75.42 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS C 538 " pdb=" SG CYS C 538 " pdb=" SG CYS C 590 " pdb=" CB CYS C 590 " ideal model delta sinusoidal sigma weight residual -86.00 -161.41 75.41 1 1.00e+01 1.00e-02 7.18e+01 dihedral pdb=" CB CYS B 840 " pdb=" SG CYS B 840 " pdb=" SG CYS B 851 " pdb=" CB CYS B 851 " ideal model delta sinusoidal sigma weight residual 93.00 25.49 67.51 1 1.00e+01 1.00e-02 5.93e+01 ... (remaining 16250 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 3288 0.079 - 0.158: 841 0.158 - 0.237: 62 0.237 - 0.315: 5 0.315 - 0.394: 10 Chirality restraints: 4206 Sorted by residual: chirality pdb=" CB THR A 33 " pdb=" CA THR A 33 " pdb=" OG1 THR A 33 " pdb=" CG2 THR A 33 " both_signs ideal model delta sigma weight residual False 2.55 2.16 0.39 2.00e-01 2.50e+01 3.88e+00 chirality pdb=" C1 NAG B1304 " pdb=" ND2 ASN B 603 " pdb=" C2 NAG B1304 " pdb=" O5 NAG B1304 " both_signs ideal model delta sigma weight residual False -2.40 -2.01 -0.39 2.00e-01 2.50e+01 3.86e+00 chirality pdb=" C2 NAG B1301 " pdb=" C1 NAG B1301 " pdb=" C3 NAG B1301 " pdb=" N2 NAG B1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.10 -0.39 2.00e-01 2.50e+01 3.84e+00 ... (remaining 4203 not shown) Planarity restraints: 4536 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN B 603 " 0.038 2.00e-02 2.50e+03 3.51e-02 1.54e+01 pdb=" CG ASN B 603 " -0.033 2.00e-02 2.50e+03 pdb=" OD1 ASN B 603 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN B 603 " -0.043 2.00e-02 2.50e+03 pdb=" C1 NAG B1304 " 0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO C 986 " -0.066 5.00e-02 4.00e+02 9.77e-02 1.53e+01 pdb=" N PRO C 987 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO C 987 " -0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 987 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 986 " 0.058 5.00e-02 4.00e+02 8.61e-02 1.19e+01 pdb=" N PRO A 987 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO A 987 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 987 " 0.049 5.00e-02 4.00e+02 ... (remaining 4533 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 3679 2.76 - 3.29: 21028 3.29 - 3.83: 39621 3.83 - 4.36: 46023 4.36 - 4.90: 82215 Nonbonded interactions: 192566 Sorted by model distance: nonbonded pdb=" O GLN B 134 " pdb=" OH TYR B 160 " model vdw 2.223 2.440 nonbonded pdb=" OG1 THR A 716 " pdb=" O GLN A1071 " model vdw 2.240 2.440 nonbonded pdb=" OG SER C 349 " pdb=" O LEU C 452 " model vdw 2.257 2.440 nonbonded pdb=" OH TYR A 91 " pdb=" OE1 GLU A 191 " model vdw 2.258 2.440 nonbonded pdb=" OG SER A 383 " pdb=" OD1 ASP B 985 " model vdw 2.262 2.440 ... (remaining 192561 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 27 through 172 or resid 186 through 250 or resid 265 throu \ gh 492 or resid 494 through 828 or resid 850 through 1147 or resid 1301 through \ 1306)) selection = (chain 'B' and (resid 27 through 250 or resid 265 through 444 or resid 447 throu \ gh 492 or resid 494 through 828 or resid 850 through 1147 or resid 1301 through \ 1306)) selection = (chain 'C' and (resid 27 through 250 or resid 265 through 492 or resid 494 throu \ gh 828 or resid 834 or resid 851 through 1147 or resid 1301 through 1306)) } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.050 Extract box with map and model: 19.500 Check model and map are aligned: 0.350 Set scattering table: 0.240 Process input model: 72.340 Find NCS groups from input model: 2.320 Set up NCS constraints: 0.360 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 112.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.117 25959 Z= 0.699 Angle : 1.061 15.447 35340 Z= 0.573 Chirality : 0.068 0.394 4206 Planarity : 0.008 0.098 4493 Dihedral : 14.381 89.439 10235 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.81 % Favored : 93.09 % Rotamer: Outliers : 0.40 % Allowed : 6.48 % Favored : 93.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.45 (0.13), residues: 3100 helix: -1.85 (0.17), residues: 681 sheet: -1.32 (0.19), residues: 619 loop : -2.95 (0.12), residues: 1800 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.051 0.005 TRP A 886 HIS 0.010 0.002 HIS A1064 PHE 0.046 0.004 PHE C 329 TYR 0.031 0.003 TYR B 495 ARG 0.007 0.001 ARG C1039 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 244 time to evaluate : 2.459 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.6621 (mtm180) cc_final: 0.6255 (mtm-85) REVERT: A 773 GLU cc_start: 0.7604 (tt0) cc_final: 0.7341 (tt0) REVERT: B 324 GLU cc_start: 0.7302 (tt0) cc_final: 0.6981 (mt-10) REVERT: B 869 MET cc_start: 0.8930 (mtt) cc_final: 0.8651 (mtt) REVERT: C 572 THR cc_start: 0.8137 (p) cc_final: 0.7673 (m) REVERT: C 811 LYS cc_start: 0.5932 (ttmt) cc_final: 0.5642 (tppp) REVERT: C 1138 TYR cc_start: 0.8004 (t80) cc_final: 0.7782 (t80) outliers start: 9 outliers final: 4 residues processed: 251 average time/residue: 1.3921 time to fit residues: 403.6566 Evaluate side-chains 167 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 2.719 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 393 THR Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain C residue 90 VAL Chi-restraints excluded: chain C residue 581 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 2.9990 chunk 236 optimal weight: 8.9990 chunk 131 optimal weight: 9.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 chunk 244 optimal weight: 6.9990 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 182 optimal weight: 0.8980 chunk 283 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A 450 ASN A 493 GLN A 563 GLN A 779 GLN A 901 GLN A 913 GLN A 926 GLN A 955 ASN A1071 GLN A1101 HIS B 66 HIS B 360 ASN B 487 ASN B 613 GLN B 675 GLN B 901 GLN B1071 GLN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C 422 ASN C 460 ASN C 751 ASN C 804 GLN C 901 GLN C 926 GLN C 960 ASN C1101 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 25959 Z= 0.169 Angle : 0.608 10.026 35340 Z= 0.313 Chirality : 0.046 0.266 4206 Planarity : 0.005 0.064 4493 Dihedral : 7.606 59.409 4652 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.97 % Favored : 95.00 % Rotamer: Outliers : 1.97 % Allowed : 10.34 % Favored : 87.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.24 (0.14), residues: 3100 helix: -0.15 (0.20), residues: 685 sheet: -0.48 (0.20), residues: 602 loop : -2.52 (0.12), residues: 1813 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 886 HIS 0.003 0.001 HIS A 519 PHE 0.021 0.001 PHE A 32 TYR 0.024 0.001 TYR A 369 ARG 0.005 0.000 ARG C 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 186 time to evaluate : 2.982 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 336 CYS cc_start: 0.5229 (OUTLIER) cc_final: 0.4760 (t) REVERT: A 654 GLU cc_start: 0.7306 (OUTLIER) cc_final: 0.7086 (pt0) REVERT: A 1145 LEU cc_start: 0.6045 (OUTLIER) cc_final: 0.5728 (mt) REVERT: B 324 GLU cc_start: 0.7326 (tt0) cc_final: 0.7116 (mt-10) REVERT: B 869 MET cc_start: 0.8797 (mtt) cc_final: 0.8581 (mtt) REVERT: C 203 ILE cc_start: 0.7744 (mt) cc_final: 0.7476 (tt) REVERT: C 224 GLU cc_start: 0.7539 (OUTLIER) cc_final: 0.5859 (mp0) REVERT: C 321 GLN cc_start: 0.7683 (OUTLIER) cc_final: 0.6744 (mp10) REVERT: C 811 LYS cc_start: 0.5800 (ttmt) cc_final: 0.5586 (tppp) REVERT: C 1050 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8134 (ptp) outliers start: 52 outliers final: 15 residues processed: 224 average time/residue: 1.1187 time to fit residues: 300.6855 Evaluate side-chains 180 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 159 time to evaluate : 2.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 640 SER Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 305 SER Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 603 ASN Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1122 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 0.7980 chunk 87 optimal weight: 0.0870 chunk 235 optimal weight: 6.9990 chunk 192 optimal weight: 8.9990 chunk 78 optimal weight: 0.9990 chunk 283 optimal weight: 6.9990 chunk 306 optimal weight: 4.9990 chunk 252 optimal weight: 10.0000 chunk 281 optimal weight: 7.9990 chunk 96 optimal weight: 1.9990 chunk 227 optimal weight: 2.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 563 GLN A1010 GLN B 360 ASN B 613 GLN B1011 GLN C 239 GLN C 409 GLN C 422 ASN C 540 ASN C 787 GLN C1101 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 25959 Z= 0.190 Angle : 0.584 9.678 35340 Z= 0.300 Chirality : 0.046 0.256 4206 Planarity : 0.004 0.051 4493 Dihedral : 6.983 57.546 4648 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.13 % Favored : 94.84 % Rotamer: Outliers : 1.97 % Allowed : 11.73 % Favored : 86.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.75 (0.14), residues: 3100 helix: 0.43 (0.21), residues: 682 sheet: -0.21 (0.20), residues: 621 loop : -2.28 (0.13), residues: 1797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 886 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE A 32 TYR 0.020 0.001 TYR A1067 ARG 0.006 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 171 time to evaluate : 3.013 Fit side-chains REVERT: A 126 VAL cc_start: 0.8417 (t) cc_final: 0.8139 (p) REVERT: A 462 LYS cc_start: 0.8012 (OUTLIER) cc_final: 0.7692 (mtpt) REVERT: A 1145 LEU cc_start: 0.6057 (OUTLIER) cc_final: 0.5745 (mt) REVERT: C 224 GLU cc_start: 0.7601 (OUTLIER) cc_final: 0.6967 (mt-10) REVERT: C 321 GLN cc_start: 0.7760 (OUTLIER) cc_final: 0.6751 (mp10) REVERT: C 646 ARG cc_start: 0.7950 (OUTLIER) cc_final: 0.7600 (mtp180) REVERT: C 1050 MET cc_start: 0.8469 (OUTLIER) cc_final: 0.8164 (ptp) REVERT: C 1138 TYR cc_start: 0.7996 (t80) cc_final: 0.7737 (t80) outliers start: 52 outliers final: 17 residues processed: 213 average time/residue: 1.0470 time to fit residues: 269.5172 Evaluate side-chains 179 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 156 time to evaluate : 2.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 5.9990 chunk 213 optimal weight: 9.9990 chunk 147 optimal weight: 30.0000 chunk 31 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 190 optimal weight: 5.9990 chunk 284 optimal weight: 0.0570 chunk 301 optimal weight: 3.9990 chunk 148 optimal weight: 3.9990 chunk 269 optimal weight: 8.9990 chunk 81 optimal weight: 3.9990 overall best weight: 3.0106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1010 GLN B 360 ASN B 613 GLN B 625 HIS ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 ASN C 409 GLN C 422 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.059 25959 Z= 0.327 Angle : 0.637 9.613 35340 Z= 0.327 Chirality : 0.048 0.259 4206 Planarity : 0.004 0.044 4493 Dihedral : 6.979 59.892 4648 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.03 % Allowed : 6.00 % Favored : 93.97 % Rotamer: Outliers : 2.29 % Allowed : 12.93 % Favored : 84.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.72 (0.14), residues: 3100 helix: 0.45 (0.21), residues: 676 sheet: -0.27 (0.20), residues: 633 loop : -2.22 (0.13), residues: 1791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP B 886 HIS 0.007 0.001 HIS A1064 PHE 0.027 0.002 PHE B 559 TYR 0.025 0.002 TYR A1067 ARG 0.005 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 162 time to evaluate : 2.665 Fit side-chains revert: symmetry clash REVERT: A 1145 LEU cc_start: 0.6153 (OUTLIER) cc_final: 0.5834 (mt) REVERT: B 581 THR cc_start: 0.7382 (OUTLIER) cc_final: 0.7177 (p) REVERT: C 224 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7198 (mt-10) REVERT: C 321 GLN cc_start: 0.7796 (OUTLIER) cc_final: 0.6825 (mp10) REVERT: C 332 ILE cc_start: 0.7905 (OUTLIER) cc_final: 0.7506 (mm) REVERT: C 448 ASN cc_start: 0.5764 (t0) cc_final: 0.5274 (t0) REVERT: C 646 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7646 (mtp180) REVERT: C 761 THR cc_start: 0.8950 (OUTLIER) cc_final: 0.8580 (p) REVERT: C 1050 MET cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (ptp) REVERT: C 1138 TYR cc_start: 0.7985 (t80) cc_final: 0.7761 (t80) outliers start: 61 outliers final: 31 residues processed: 209 average time/residue: 0.9825 time to fit residues: 251.6359 Evaluate side-chains 194 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 155 time to evaluate : 2.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 493 GLN Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 804 GLN Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 51 THR Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 428 ASP Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 9.9990 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 224 optimal weight: 0.9980 chunk 124 optimal weight: 0.6980 chunk 257 optimal weight: 10.0000 chunk 208 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 153 optimal weight: 8.9990 chunk 270 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 GLN A1010 GLN B 360 ASN B 613 GLN C 409 GLN C 422 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8085 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25959 Z= 0.187 Angle : 0.576 9.586 35340 Z= 0.295 Chirality : 0.047 0.741 4206 Planarity : 0.004 0.054 4493 Dihedral : 6.652 57.392 4648 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.03 % Allowed : 5.26 % Favored : 94.71 % Rotamer: Outliers : 2.33 % Allowed : 13.40 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.46 (0.15), residues: 3100 helix: 0.70 (0.21), residues: 692 sheet: -0.16 (0.20), residues: 643 loop : -2.08 (0.13), residues: 1765 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 886 HIS 0.003 0.001 HIS C1064 PHE 0.021 0.001 PHE A 32 TYR 0.022 0.001 TYR A 453 ARG 0.005 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 164 time to evaluate : 2.466 Fit side-chains REVERT: A 126 VAL cc_start: 0.8409 (t) cc_final: 0.8110 (p) REVERT: A 462 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: A 468 ILE cc_start: 0.6140 (OUTLIER) cc_final: 0.5914 (pt) REVERT: A 740 MET cc_start: 0.7811 (tpp) cc_final: 0.7611 (tpt) REVERT: A 1145 LEU cc_start: 0.6112 (OUTLIER) cc_final: 0.5830 (mt) REVERT: B 234 ASN cc_start: 0.5013 (OUTLIER) cc_final: 0.4669 (p0) REVERT: B 324 GLU cc_start: 0.7317 (mt-10) cc_final: 0.6862 (mp0) REVERT: B 581 THR cc_start: 0.7295 (OUTLIER) cc_final: 0.7012 (p) REVERT: C 224 GLU cc_start: 0.7653 (OUTLIER) cc_final: 0.7061 (mt-10) REVERT: C 321 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.6785 (mp10) REVERT: C 332 ILE cc_start: 0.7814 (OUTLIER) cc_final: 0.7445 (mm) REVERT: C 646 ARG cc_start: 0.7958 (OUTLIER) cc_final: 0.7596 (mtp180) REVERT: C 1050 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8144 (ptp) REVERT: C 1138 TYR cc_start: 0.7967 (t80) cc_final: 0.7759 (t80) outliers start: 62 outliers final: 31 residues processed: 215 average time/residue: 1.0106 time to fit residues: 264.9147 Evaluate side-chains 194 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 153 time to evaluate : 2.587 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 553 THR Chi-restraints excluded: chain A residue 571 ASP Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 332 ILE Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 859 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 8.9990 chunk 271 optimal weight: 2.9990 chunk 59 optimal weight: 8.9990 chunk 177 optimal weight: 0.6980 chunk 74 optimal weight: 3.9990 chunk 301 optimal weight: 3.9990 chunk 250 optimal weight: 0.0970 chunk 139 optimal weight: 30.0000 chunk 25 optimal weight: 0.0000 chunk 99 optimal weight: 0.9980 chunk 158 optimal weight: 10.0000 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 493 GLN B 360 ASN B 613 GLN C 360 ASN C 409 GLN C 422 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.061 25959 Z= 0.159 Angle : 0.539 9.572 35340 Z= 0.274 Chirality : 0.045 0.406 4206 Planarity : 0.004 0.056 4493 Dihedral : 5.936 56.096 4648 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.03 % Allowed : 4.87 % Favored : 95.10 % Rotamer: Outliers : 2.18 % Allowed : 14.02 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.17 (0.15), residues: 3100 helix: 1.10 (0.21), residues: 686 sheet: 0.08 (0.20), residues: 630 loop : -1.97 (0.14), residues: 1784 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.003 0.001 HIS C 519 PHE 0.020 0.001 PHE C 32 TYR 0.021 0.001 TYR A 453 ARG 0.005 0.000 ARG B1107 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 173 time to evaluate : 2.896 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8337 (t) cc_final: 0.8036 (p) REVERT: A 132 GLU cc_start: 0.7355 (OUTLIER) cc_final: 0.7074 (mt-10) REVERT: A 468 ILE cc_start: 0.6122 (OUTLIER) cc_final: 0.5909 (pt) REVERT: A 1145 LEU cc_start: 0.6121 (OUTLIER) cc_final: 0.5885 (mt) REVERT: B 234 ASN cc_start: 0.5020 (OUTLIER) cc_final: 0.4640 (p0) REVERT: B 324 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6840 (mp0) REVERT: C 224 GLU cc_start: 0.7451 (OUTLIER) cc_final: 0.6894 (mt-10) REVERT: C 629 LEU cc_start: 0.3328 (OUTLIER) cc_final: 0.2861 (mp) REVERT: C 646 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7610 (mtp180) REVERT: C 761 THR cc_start: 0.8637 (OUTLIER) cc_final: 0.8347 (p) REVERT: C 1050 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8028 (ptp) REVERT: C 1138 TYR cc_start: 0.7946 (t80) cc_final: 0.7731 (t80) outliers start: 58 outliers final: 26 residues processed: 221 average time/residue: 1.1076 time to fit residues: 294.4491 Evaluate side-chains 189 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 154 time to evaluate : 2.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 916 LEU Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1145 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 629 LEU Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 171 optimal weight: 2.9990 chunk 220 optimal weight: 0.8980 chunk 170 optimal weight: 0.8980 chunk 254 optimal weight: 10.0000 chunk 168 optimal weight: 5.9990 chunk 300 optimal weight: 3.9990 chunk 188 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 138 optimal weight: 5.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 804 GLN A1010 GLN B 360 ASN B 613 GLN C 360 ASN C 409 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.079 25959 Z= 0.205 Angle : 0.560 9.957 35340 Z= 0.286 Chirality : 0.046 0.347 4206 Planarity : 0.004 0.052 4493 Dihedral : 5.913 56.834 4648 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.22 % Allowed : 14.38 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3100 helix: 1.06 (0.21), residues: 687 sheet: 0.15 (0.20), residues: 638 loop : -1.94 (0.13), residues: 1775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.021 0.001 PHE A 32 TYR 0.025 0.001 TYR C 904 ARG 0.002 0.000 ARG A1019 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 159 time to evaluate : 2.877 Fit side-chains REVERT: A 126 VAL cc_start: 0.8381 (t) cc_final: 0.8074 (p) REVERT: A 132 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.7086 (mt-10) REVERT: A 468 ILE cc_start: 0.6010 (OUTLIER) cc_final: 0.5781 (pt) REVERT: B 234 ASN cc_start: 0.5168 (OUTLIER) cc_final: 0.4746 (p0) REVERT: B 324 GLU cc_start: 0.7296 (mt-10) cc_final: 0.6873 (mp0) REVERT: B 581 THR cc_start: 0.7278 (OUTLIER) cc_final: 0.7014 (p) REVERT: C 224 GLU cc_start: 0.7483 (OUTLIER) cc_final: 0.6938 (mt-10) REVERT: C 321 GLN cc_start: 0.7754 (OUTLIER) cc_final: 0.6996 (mp10) REVERT: C 646 ARG cc_start: 0.7979 (OUTLIER) cc_final: 0.7616 (mtp180) REVERT: C 761 THR cc_start: 0.8752 (OUTLIER) cc_final: 0.8445 (p) REVERT: C 1050 MET cc_start: 0.8383 (OUTLIER) cc_final: 0.8083 (ptp) outliers start: 59 outliers final: 30 residues processed: 210 average time/residue: 1.0922 time to fit residues: 280.0754 Evaluate side-chains 192 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 153 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 227 VAL Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1081 ILE Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 179 optimal weight: 6.9990 chunk 90 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 58 optimal weight: 0.5980 chunk 191 optimal weight: 2.9990 chunk 204 optimal weight: 6.9990 chunk 148 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 360 ASN B 613 GLN B 628 GLN C 99 ASN ** C 196 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 409 GLN C1101 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 25959 Z= 0.215 Angle : 0.567 12.551 35340 Z= 0.289 Chirality : 0.046 0.326 4206 Planarity : 0.004 0.046 4493 Dihedral : 5.910 57.542 4648 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.22 % Allowed : 14.86 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.13 (0.15), residues: 3100 helix: 1.02 (0.21), residues: 686 sheet: 0.11 (0.20), residues: 642 loop : -1.90 (0.13), residues: 1772 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.022 0.001 PHE A 32 TYR 0.028 0.001 TYR C 904 ARG 0.002 0.000 ARG A1000 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 161 time to evaluate : 2.812 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8398 (t) cc_final: 0.8112 (p) REVERT: A 132 GLU cc_start: 0.7366 (OUTLIER) cc_final: 0.7065 (mt-10) REVERT: A 360 ASN cc_start: 0.5902 (m-40) cc_final: 0.5482 (t0) REVERT: A 468 ILE cc_start: 0.6027 (OUTLIER) cc_final: 0.5734 (pt) REVERT: B 234 ASN cc_start: 0.5077 (OUTLIER) cc_final: 0.4659 (p0) REVERT: B 324 GLU cc_start: 0.7350 (mt-10) cc_final: 0.6925 (mp0) REVERT: C 224 GLU cc_start: 0.7531 (OUTLIER) cc_final: 0.7146 (mt-10) REVERT: C 321 GLN cc_start: 0.7767 (OUTLIER) cc_final: 0.7011 (mp10) REVERT: C 646 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7619 (mtp180) REVERT: C 761 THR cc_start: 0.8816 (OUTLIER) cc_final: 0.8499 (p) REVERT: C 1050 MET cc_start: 0.8457 (OUTLIER) cc_final: 0.8168 (ptp) outliers start: 59 outliers final: 36 residues processed: 207 average time/residue: 1.0516 time to fit residues: 263.9340 Evaluate side-chains 199 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 155 time to evaluate : 2.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 THR Chi-restraints excluded: chain A residue 30 ASN Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 546 LEU Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 602 THR Chi-restraints excluded: chain A residue 618 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 723 THR Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1123 SER Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 553 THR Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 224 GLU Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 307 THR Chi-restraints excluded: chain C residue 321 GLN Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 622 VAL Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 705 VAL Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1050 MET Chi-restraints excluded: chain C residue 1139 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 0.0770 chunk 288 optimal weight: 0.8980 chunk 262 optimal weight: 6.9990 chunk 280 optimal weight: 4.9990 chunk 168 optimal weight: 0.6980 chunk 122 optimal weight: 0.0870 chunk 220 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 253 optimal weight: 20.0000 chunk 265 optimal weight: 7.9990 chunk 279 optimal weight: 0.6980 overall best weight: 0.4916 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 448 ASN A1005 GLN A1010 GLN B 360 ASN B 613 GLN C 409 GLN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.057 25959 Z= 0.135 Angle : 0.528 11.625 35340 Z= 0.269 Chirality : 0.044 0.282 4206 Planarity : 0.004 0.046 4493 Dihedral : 5.563 56.318 4648 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 1.38 % Allowed : 16.10 % Favored : 82.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.15), residues: 3100 helix: 1.32 (0.22), residues: 686 sheet: 0.29 (0.20), residues: 647 loop : -1.84 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 436 HIS 0.002 0.000 HIS C 519 PHE 0.010 0.001 PHE A 562 TYR 0.024 0.001 TYR C 904 ARG 0.004 0.000 ARG C 237 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 169 time to evaluate : 3.244 Fit side-chains revert: symmetry clash REVERT: A 126 VAL cc_start: 0.8295 (t) cc_final: 0.8027 (p) REVERT: A 132 GLU cc_start: 0.7374 (OUTLIER) cc_final: 0.7154 (mt-10) REVERT: A 360 ASN cc_start: 0.5738 (m-40) cc_final: 0.5367 (t0) REVERT: A 468 ILE cc_start: 0.6041 (OUTLIER) cc_final: 0.5694 (pt) REVERT: A 855 PHE cc_start: 0.7003 (m-10) cc_final: 0.6524 (m-80) REVERT: B 234 ASN cc_start: 0.5050 (OUTLIER) cc_final: 0.4663 (p0) REVERT: B 324 GLU cc_start: 0.7285 (mt-10) cc_final: 0.6885 (mp0) REVERT: C 190 ARG cc_start: 0.6476 (OUTLIER) cc_final: 0.5674 (tpp-160) REVERT: C 646 ARG cc_start: 0.7967 (OUTLIER) cc_final: 0.7631 (mtp180) REVERT: C 1050 MET cc_start: 0.8258 (OUTLIER) cc_final: 0.7979 (ptp) outliers start: 36 outliers final: 24 residues processed: 200 average time/residue: 1.1228 time to fit residues: 272.4516 Evaluate side-chains 184 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 154 time to evaluate : 2.567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 347 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 524 VAL Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 190 ARG Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 632 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 3.9990 chunk 296 optimal weight: 3.9990 chunk 180 optimal weight: 0.9980 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 4.9990 chunk 310 optimal weight: 0.9990 chunk 286 optimal weight: 4.9990 chunk 247 optimal weight: 0.0070 chunk 25 optimal weight: 20.0000 chunk 191 optimal weight: 4.9990 chunk 151 optimal weight: 6.9990 overall best weight: 1.8004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 360 ASN B 613 GLN B 690 GLN C 409 GLN C 540 ASN C1101 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 25959 Z= 0.221 Angle : 0.565 11.613 35340 Z= 0.288 Chirality : 0.046 0.288 4206 Planarity : 0.004 0.044 4493 Dihedral : 5.692 57.004 4648 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 1.60 % Allowed : 16.06 % Favored : 82.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.15), residues: 3100 helix: 1.15 (0.21), residues: 688 sheet: 0.28 (0.20), residues: 648 loop : -1.84 (0.14), residues: 1764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.020 0.001 PHE A 32 TYR 0.031 0.001 TYR C 904 ARG 0.006 0.000 ARG C 237 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6200 Ramachandran restraints generated. 3100 Oldfield, 0 Emsley, 3100 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 159 time to evaluate : 3.104 Fit side-chains REVERT: A 126 VAL cc_start: 0.8375 (t) cc_final: 0.8074 (p) REVERT: A 132 GLU cc_start: 0.7411 (OUTLIER) cc_final: 0.7170 (mt-10) REVERT: A 360 ASN cc_start: 0.5925 (m-40) cc_final: 0.5490 (t0) REVERT: A 468 ILE cc_start: 0.5881 (OUTLIER) cc_final: 0.5565 (pt) REVERT: A 697 MET cc_start: 0.8277 (ptp) cc_final: 0.8063 (ptm) REVERT: B 234 ASN cc_start: 0.5108 (OUTLIER) cc_final: 0.4733 (p0) REVERT: B 324 GLU cc_start: 0.7346 (mt-10) cc_final: 0.6923 (mp0) REVERT: C 646 ARG cc_start: 0.7970 (OUTLIER) cc_final: 0.7612 (mtp180) REVERT: C 761 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8485 (p) REVERT: C 1050 MET cc_start: 0.8412 (OUTLIER) cc_final: 0.8107 (ptp) outliers start: 42 outliers final: 23 residues processed: 192 average time/residue: 1.1212 time to fit residues: 260.1577 Evaluate side-chains 181 residues out of total 2744 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 152 time to evaluate : 2.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 VAL Chi-restraints excluded: chain A residue 132 GLU Chi-restraints excluded: chain A residue 338 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 468 ILE Chi-restraints excluded: chain A residue 547 THR Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 654 GLU Chi-restraints excluded: chain A residue 759 PHE Chi-restraints excluded: chain A residue 883 THR Chi-restraints excluded: chain A residue 1094 VAL Chi-restraints excluded: chain A residue 1122 VAL Chi-restraints excluded: chain A residue 1141 LEU Chi-restraints excluded: chain B residue 234 ASN Chi-restraints excluded: chain B residue 581 THR Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 622 VAL Chi-restraints excluded: chain B residue 747 THR Chi-restraints excluded: chain B residue 1118 ASP Chi-restraints excluded: chain B residue 1127 ASP Chi-restraints excluded: chain C residue 83 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 432 CYS Chi-restraints excluded: chain C residue 459 SER Chi-restraints excluded: chain C residue 581 THR Chi-restraints excluded: chain C residue 635 VAL Chi-restraints excluded: chain C residue 646 ARG Chi-restraints excluded: chain C residue 761 THR Chi-restraints excluded: chain C residue 1050 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 3.9990 chunk 263 optimal weight: 0.9980 chunk 75 optimal weight: 1.9990 chunk 228 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 247 optimal weight: 6.9990 chunk 103 optimal weight: 20.0000 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1010 GLN B 360 ASN B 613 GLN C 409 GLN C1101 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.192587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.151474 restraints weight = 33525.401| |-----------------------------------------------------------------------------| r_work (start): 0.3732 rms_B_bonded: 2.14 r_work: 0.3320 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work (final): 0.3320 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3227 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3227 r_free = 0.3227 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3227 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 25959 Z= 0.199 Angle : 0.557 11.349 35340 Z= 0.284 Chirality : 0.046 0.288 4206 Planarity : 0.004 0.044 4493 Dihedral : 5.695 57.263 4648 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer: Outliers : 1.53 % Allowed : 16.17 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.96 (0.15), residues: 3100 helix: 1.11 (0.21), residues: 688 sheet: 0.29 (0.20), residues: 645 loop : -1.82 (0.14), residues: 1767 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.004 0.001 HIS A1064 PHE 0.023 0.001 PHE A 32 TYR 0.035 0.001 TYR C 904 ARG 0.004 0.000 ARG C 237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6869.13 seconds wall clock time: 126 minutes 19.95 seconds (7579.95 seconds total)